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http://en.wikipedia.org/wiki/Catharism
The crusader army came under the command, both spiritually and militarily, of the papal legate Arnaud-Amaury, Abbot of Cîteaux. In the first significant engagement of the war, the town of Béziers was besieged on 22 July 1209. The Catholic inhabitants of the city were granted the freedom to leave unharmed, but many refused and opted to stay and fight alongside the Cathars.

The Cathars spent much of 1209 fending off the crusaders. The Béziers army attempted a sortie but was quickly defeated, then pursued by the crusaders back through the gates and into the city. Arnaud, the Cistercian abbot-commander, is supposed to have been asked how to tell Cathars from Catholics. His reply, recalled by Caesar of Heisterbach, a fellow Cistercian, thirty years later was "Caedite eos. Novit enim Dominus qui sunt eius."—"Kill them all, the Lord will recognise His own." The doors of the church of St Mary Magdalene were broken down and the refugees dragged out and slaughtered. Reportedly, 7,000 people died there. Elsewhere in the town many more thousands were mutilated and killed. Prisoners were blinded, dragged behind horses, and used for target practice.[35] What remained of the city was razed by fire. Arnaud wrote to Pope Innocent III, "Today your Holiness, twenty thousand heretics were put to the sword, regardless of rank, age, or sex." The permanent population of Béziers at that time was then probably no more than 5,000, but local refugees seeking shelter within the city walls could conceivably have increased the number to 20,000.

After the success of his siege of Carcassonne, which followed the Massacre at Béziers in 1209, Simon de Montfort was designated as leader of the Crusader army. Prominent opponents of the Crusaders were Raymond Roger Trencavel, viscount of Carcassonne, and his feudal overlord Peter II, the king of Aragon, who held fiefdoms and had a number of vassals in the region. Peter died fighting against the crusade on 12 September 1213 at the Battle of Muret. de Montfort was killed on 25 June 1218 after maintaining a siege of Toulouse for nine months.[38]
Treaty and persecution

The war ended in the Treaty of Paris (1229), by which the king of France dispossessed the house of Toulouse of the greater part of its fiefs, and that of the Trencavels (Viscounts of Béziers and Carcassonne) of the whole of their fiefs. The independence of the princes of the Languedoc was at an end. But in spite of the wholesale massacre of Cathars during the war, Catharism was not yet extinguished.

In 1215, the bishops of the Catholic Church met at the Fourth Council of the Lateran under Pope Innocent III. One of the key goals of the council was to combat the heresy of the Cathars.

The Inquisition was established in 1229 to uproot the remaining Cathars. Operating in the south at Toulouse, Albi, Carcassonne and other towns during the whole of the 13th century, and a great part of the 14th, it finally succeeded in extirpating the movement. Cathars who refused to recant were hanged, or burnt at the stake.

From May 1243 to March 1244, the Cathar fortress of Montségur was besieged by the troops of the seneschal of Carcassonne and the archbishop of Narbonne. On 16 March 1244, a large and symbolically important massacre took place, where over 200 Cathar Perfects were burnt in an enormous fire at the prat dels cremats near the foot of the castle. Moreover, the Church decreed lesser chastisements against laymen suspected of sympathy with Cathars, at the 1235 Council of Narbonne.